Long as you could set it so each object could have it's own strength of gravity...
Per say like a giant base asteroid has a greater gravity effect than it's miniature brethren.
The rest should sort itself out with inertia, and acceleration right?
I can come up with a reason for having greater gravitational influence on capships though.
Wing Commander's dropping of a Kilrathi crusier into the star... the fighter escaped
while the larger ship did not.

Might be a bit of a bonus if you set a mission in a area where there were many
powerful gravitational forces at play or had an interdictor present. It would require
that your capships move a little slower or differently than normal.